# Phylogenomics of the Rarest Animals: A second species of Micrognathozoa identified by machine learning
This is the first phylgoenomic study of the intraphylum relationships in Micrognathozoa.
We generated transcriptomes from single animals across multiple specimens in all three known populations,
investivated the phylogenetic relationships, tested species limits, and inferred their biogeographic history.


### Figure
These are the full size files of all the figures in the paper.
- Fig1 FINAL.tif
- Fig2 FINAL.tif
- Fig3 FINAL.tif

### Code Version
- R 4.4.0
- Python 3.12.4
- See main text for program versions

### Phylogenomics
**Data Files**
- M1.partitions
- M1.phylip
- M2.partitions
- M2.phylip

**Output Files**
- M1_ExaBayes.tre
- M1_IQTREE.tre
- M2_ExaBayes.tre
- M2_IQTREE.tre

### Dating Analysis
**Input Files**
- Limnognathia_COI_18S.nex

**Output Files**
- Limno_dating.log
- Limno_dating.trees
- Limno_dating.xml
- Limno_dating_MCC.tree

### UML
**VAE Input Files**
- M3.txt
- M5.txt
- M6.txt
- M7.txt
- M8.txt
- M9.txt

**PCA, RF, tSNE Input Files**
- M4.vcf
- UML_clustering.R

### GMYC
__NOTE: Input alignment is Limno_dating_MCC.tree__
- gmyc.R

### CLADES
**Data Files**
- M10.txt
**Outut Files**
- CLADES_analysis1.out
- CLADES_analysis2.out
- CLADES_analysis3.out

**Custom Rotifer Input Files**
- Rotifer_CLADES_dataset.txt

**Custom Rotifer Model Files**
- custom_dataset.out
- custom_dataset.range
- custom_dataset.sumstat
- custom_dataset.sumstat.scale
- custom_dataset.sumstat.scale.model

### SNAPPER
**Input files**
__NOTE: Input alignment is M4.txt__
- Limno_SNAPPER_2sp.xml
- Limno_SNAPPER_3sp.xml

### DelimitR
__NOTE: Input alignment is M4.txt__
- delimitr.R

### Admixture
__NOTE: Input alignment is M4.txt__
- admixture.sh

### Molecular Species Description
**18S rRNA**
- 18S_reference.fasta
- 18SrRNA.vcf

**COI**
- COI_alignment.fasta
- COI_alignment_trimmed.fasta

### Other Scripts
- fixrcorrector.py
- getting_SNPs.sh
- orthofinder-phylopyruner.sh
- randSNPs_from_vcf.pl
- vcf2phylip.py
- OneHotEncode.py
